The hepatitis C virus (HCV) poses a public health threat. It is important to identify viral factors that thwart natural defenses and contribute to treatment failure. In a cross sectional study, we recently found an inverse relationship between viral replication and the presence of antibodies directed against HCV's novel alternate reading frame proteins (ARFPs). ARFPs were discovered previously by our group. The spike of anti-ARFP antibodies suggests that production of ARFPs is increased when HCV replication is inhibited. HCV RNAs of patients with anti-ARFP antibodies have mutations in a putative cis regulatory element (CRE) called the Terminal Stem-loops, an RNA structure we also discovered previously. Our recent results suggest that ARFPs may help HCV survive adverse conditions, and indicate that CREs may control the production of ARFPs. The proposed studies are based on our recent data, and on data of others showing that HCV RNAs of patients with advanced cirrhosis and liver cancer have mutations in the Terminal Stem-loops. Experiments in Aim I test the hypothesis that effective anti-viral responses induced by IFN/ribavirin treatment are marked by a rise in immune responses to ARFPs. HCV RNA and anti-ARFP antibody levels, and the stimulation index (SI) and phenotype of peripheral blood mononuclear cells will be compared before, during, and after treatment. Experiments in Aim 2 test the hypothesis that mutations in the Terminal Stem-loops element accumulate during IFN/ribavirin treatment and during progression to advanced liver disease and liver cancer, modulating its function and increasing production of ARFPs. New software will be developed and applied to an expanded dataset of mutations, and the structure/function relationships of the Terminal Stem-loops will be defined. New information about HCV's adaptive mechanisms and pathways of gene expression will emerge from these studies and will advance the development of new drugs and vaccines for HCV.